Read this with great interest. I use a Denon 4311 with La Scalas (F), Fortes (Wides), KT-LCR ©, SS 1 (Heights and back), RS 3 (surround) and 2 DIY subs.
All Audyssey is trying to do is get the reference volume for all speakers set to 75db where the mic is located. The sub is in the same boat. In other words, the level of any speaker (including the sub) doesn't have anything to do with any other speaker...they are all trying to get to 75db at the listening position (which is the first mic position).
If all the speakers are at -12db, then you need to put the mic further away. Point the mic straight up. If they are still out of whack, you'll need to get a Radio Shack meter and adjust the levels manually. Nothing wrong with that at all. All it means is that when your volume is at 0 (on the relative scale which equats to 75db), you'll actually be listening at a louder level. (Example: Audyssey sets your La Scalas at -12. You adjust all the speakers with the Radio Shack meter and the La Scalas end up at -8. When you set the volume control to 0, you'll be at 79db instead of 75db.) Usually no one complains if its a little louder.
I always tweak my levels (some call them trims) for each channel with the rat shack meter. Usually involve bumping the center 1 or 2 db and bumping the sub 4-5 db.